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Database Commons - ENCODE

ENCODE

Citations: 2053

z-index 27.86

Short name ENCODE
Full name Encyclopedia of DNA Elements
Description The ENCODE Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome,including elements that act at the protein and RNA levels,and regulatory elements that control cells and circumstances in which a gene is active.
URL https://www.encodeproject.org/
Year founded 2004
Last update & version 2017-02-03    
Availability Free to all users
University/Institution hosted Stanford University School of Medicine
Address Department of Genetics
City Stanford
Province/State CA
Country/Region United States
Contact name J. Michael Cherry
Contact email cherry@stanford.edu
Data type(s)
Major organism(s)
Keyword(s)
  • functional element
  • human genome
  • NHGRI
  • regulatory element
Publication(s)
  • Principles of metadata organization at the ENCODE data coordination center. [PMID: 26980513]

    Eurie L Hong, Cricket A Sloan, Esther T Chan, Jean M Davidson, Venkat S Malladi, J Seth Strattan, Benjamin C Hitz, Idan Gabdank, Aditi K Narayanan, Marcus Ho, Brian T Lee, Laurence D Rowe, Timothy R Dreszer, Greg R Roe, Nikhil R Podduturi, Forrest Tanaka, Jason A Hilton, J Michael Cherry
    Database : the journal of biological databases and curation 2016:2016
    3 Citations (Google Scholar as of 2017-03-07)

    Abstract: The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/). Database URL: www.encodeproject.org. © The Author(s) 2016. Published by Oxford University Press.

  • ENCODE data at the ENCODE portal. [PMID: 26527727]

    Cricket A Sloan, Esther T Chan, Jean M Davidson, Venkat S Malladi, J Seth Strattan, Benjamin C Hitz, Idan Gabdank, Aditi K Narayanan, Marcus Ho, Brian T Lee, Laurence D Rowe, Timothy R Dreszer, Greg Roe, Nikhil R Podduturi, Forrest Tanaka, Eurie L Hong, J Michael Cherry
    Nucleic acids research 2016:44(D1)
    22 Citations (Google Scholar as of 2017-03-07)

    Abstract: The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • ENCODE data in the UCSC Genome Browser: year 5 update. [PMID: 23193274]

    Kate R Rosenbloom, Cricket A Sloan, Venkat S Malladi, Timothy R Dreszer, Katrina Learned, Vanessa M Kirkup, Matthew C Wong, Morgan Maddren, Ruihua Fang, Steven G Heitner, Brian T Lee, Galt P Barber, Rachel A Harte, Mark Diekhans, Jeffrey C Long, Steven P Wilder, Ann S Zweig, Donna Karolchik, Robert M Kuhn, David Haussler, W James Kent
    Nucleic acids research 2013:41(Database issue)
    408 Citations (Google Scholar as of 2017-03-07)

    Abstract: The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.

  • ENCODE whole-genome data in the UCSC Genome Browser: update 2012. [PMID: 22075998]

    Kate R Rosenbloom, Timothy R Dreszer, Jeffrey C Long, Venkat S Malladi, Cricket A Sloan, Brian J Raney, Melissa S Cline, Donna Karolchik, Galt P Barber, Hiram Clawson, Mark Diekhans, Pauline A Fujita, Mary Goldman, Robert C Gravell, Rachel A Harte, Angie S Hinrichs, Vanessa M Kirkup, Robert M Kuhn, Katrina Learned, Morgan Maddren, Laurence R Meyer, Andy Pohl, Brooke Rhead, Matthew C Wong, Ann S Zweig, David Haussler, W James Kent
    Nucleic acids research 2012:40(Database issue)
    196 Citations (Google Scholar as of 2017-03-07)

    Abstract: The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genome-preview.ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets.

  • ENCODE whole-genome data in the UCSC genome browser (2011 update). [PMID: 21037257]

    Brian J Raney, Melissa S Cline, Kate R Rosenbloom, Timothy R Dreszer, Katrina Learned, Galt P Barber, Laurence R Meyer, Cricket A Sloan, Venkat S Malladi, Krishna M Roskin, Bernard B Suh, Angie S Hinrichs, Hiram Clawson, Ann S Zweig, Vanessa Kirkup, Pauline A Fujita, Brooke Rhead, Kayla E Smith, Andy Pohl, Robert M Kuhn, Donna Karolchik, David Haussler, W James Kent
    Nucleic acids research 2011:39(Database issue)
    172 Citations (Google Scholar as of 2017-03-07)

    Abstract: The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access.

  • ENCODE whole-genome data in the UCSC Genome Browser. [PMID: 19920125]

    Kate R Rosenbloom, Timothy R Dreszer, Michael Pheasant, Galt P Barber, Laurence R Meyer, Andy Pohl, Brian J Raney, Ting Wang, Angie S Hinrichs, Ann S Zweig, Pauline A Fujita, Katrina Learned, Brooke Rhead, Kayla E Smith, Robert M Kuhn, Donna Karolchik, David Haussler, W James Kent
    Nucleic acids research 2010:38(Database issue)
    229 Citations (Google Scholar as of 2017-03-07)

    Abstract: The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access.

  • The ENCODE (ENCyclopedia Of DNA Elements) Project. [PMID: 15499007]

    Science (New York, N.Y.) 2004:306(5696)
    1023 Citations (Google Scholar as of 2017-03-07)

    Abstract: The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.

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Tags

DNA Protein RNA
Homo sapiens Mus musculus
functional element human genome NHGRI regulatory element

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-03-07]
    • Lina Ma [2016-04-08]
    • Jian Sang [2016-04-04]
    • Lin Liu [2016-01-29]
    • Lin Liu [2016-01-15]
    • Jian Sang [2015-12-08]
    • Jian Sang [2015-06-27]
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